In settling, Walgreens neither admits nor denies the allegations. The SEC was investigating whether the drugstore chain's former chief executive and former chief financial officer failed to provide adequate warning about the risks associated with Walgreens' planned merger with Alliance Boots.

The SEC alleged the two former executives, then-CEO Greg Wasson and then-CFO Wade Miquelon, acted "negligently" when giving financial forecasts in June, October and December of 2013 and March of 2014 during earnings calls. Both Wasson and Miquelon are ordered to pay a $160,000 fine.

When Walgreens announced a two-step merger with Alliance Boots in June 2012, it projected the combined company would generate $9 billion to $9.5 billion in combined adjusted operating income in the 2016 fiscal year. However, the SEC alleged that after completing the first step of the merger, Walgreens' internal forecasts showed the company was at a "significantly" greater risk of missing those estimates.

Yet the two executives publicly reaffirmed the forecasts, the SEC alleged.

By November 2013, Walgreens had realized that an unanticipated increase in price of generic drugs would put further pressure on Walgreens' "already lagging" pharmacy business, the SEC said. The company lowered its fiscal 2016 forecast on Dec. 13. Since management was aware of the risk prior to December 2013, Walgreens' disclosures "failed to adequately disclose the increase in the risk," the agency said.

In this Feb. 23, 2013 file photo, Walgreen Co. President and CEO Greg Wasson speaks during the National Governors Association Winter Meeting in Washington. Walgreen says Wasson will retire after the drugstore chain completes its merger with health and beauty retailer Alliance Boots. Walgreen expects that deal to close during the first quarter of 2015. The largest U.S. drugstore operator says Alliance Boots Chairman Stefano Pessina will become its acting CEO.(Photo: Manuel Balce Ceneta, AP)

Then in 2014 Walgreens decided its 2016 operating income goal was "no longer reasonably attainable." It withdrew those goals on its June 24 earnings call and told investors it would soon provide a new set of goals.

The next month, on Aug. 6, Walgreens gave a new earnings per share estimate that translated to an adjusted operating income of $7.2 billion for fiscal year 2016, a 20 percent decline from its initial estimate. Shares fell 14.3 percent when Walgreens announced the new financial targets, according to the SEC.

"Over multiple reporting periods, senior Walgreens executives misled investors about the company's public financial goal," Stephanie Avakian, co-director of the SEC's Division of Enforcement, said in a statement. "The penalty assessed against Walgreens is intended to punish and deter such conduct, which deprived investors of information necessary to make fully informed investment decisions."

Walgreens in 2012 took a 45 percent stake in Alliance Boots for $6.7 billion with the option to later buy the remaining 55 percent. It closed the complete transaction at the end of 2014.

Wasson started as Walgreens' CEO in 2009 and left in 2015 when the merger with Alliance Boots closed and current CEO Stefano Pessina took the helm of the combined company. Miquelon served as Walgreens' CFO from 2008 and departed in August 2014.